Methods for genome assembly and haplotype phasing

ABSTRACT

The disclosure provides methods to assemble genomes of eukaryotic or prokaryotic organisms. The disclosure further provides methods for haplotype phasing and meta-genomics assemblies.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.15/167,880, filed May 27, 2016, which is a continuation of U.S. patentapplication Ser. No. 14/170,339, filed Jan. 31, 2014, which applicationclaims priority under 35 U.S.C. § 119 from Provisional Application Ser.No. 61/759,941, filed Feb. 1, 2013, the disclosures of which areincorporated herein by reference.

TECHNICAL FIELD

The disclosure provides for methods of genome assembly and haplotypephasing for identifying short, intermediate and long term connectionswithin a genome.

BACKGROUND

It remains difficult in theory and in practice to produce high-quality,highly contiguous genome sequences.

SUMMARY

The disclosure provides methods for accelerating and improving de novogenome assembly. The methods disclosed herein utilize methods for dataanalysis that allow for rapid and inexpensive de novo assembly ofgenomes from one or more subjects. The disclosure further provides thatthe methods disclosed herein can be used in a variety of applications,including haplotype phasing, and metagenomics analysis.

In a certain embodiment, the disclosure provides for a method for genomeassembly comprising the steps of: generating a plurality of contigs;generating a plurality of read pairs from data produced by probing thephysical layout of chromosomes, chromatin, or reconstituted chromatin;mapping or assembling the plurality of read pairs to the plurality ofcontigs; constructing an adjacency matrix of contigs using theread-mapping or assembly data; and analyzing the adjacency matrix todetermine a path through the contigs that represent their order and/ororientation to the genome. In a further embodiment, the disclosureprovides that each read pair is weighted by taking a function of eachread's distance to the edge of the contig so as to incorporateinformation about which read pairs indicate short-range contacts andwhich read pairs indicate longer-range contacts. In another embodiment,the adjacency matrix can be re-scaled to down-weight the high number ofcontacts on some contigs that represent promiscuous regions of thegenome, such as conserved binding sites for one or more agents thatregulate the scaffolding interactions of chromatin, like transcriptionalrepressor CTCF. In another embodiment, the disclosure provides for amethod for the genome assembly of a human subject, whereby the pluralityof contigs is generated from the human subject's DNA, and whereby theplurality of read pairs is generated from analyzing the human subject'schromosomes, chromatin, or reconstituted chromatin made from thesubject's naked DNA.

In a further embodiment, the disclosure provides that a plurality ofcontigs can be generated by using a shotgun sequencing methodcomprising: fragmenting long stretches of a subject's DNA into randomfragments of indeterminate size; sequencing the fragments using highthroughput sequencing methods to generate a plurality of sequencingreads; and assembling the sequencing reads so as to form a plurality ofcontigs.

In a certain embodiment, the disclosure provides that a plurality ofread pairs can be generated by probing the physical layout ofchromosomes, chromatin, or reconstituted chromatin using a Hi-C basedtechnique. In a further embodiment, the Hi-C based technique comprises,crosslinking chromosomes, chromatin, or reconstituted chromatin with afixative agent, such as formaldehyde, to form DNA-protein cross links;cutting the cross-linked DNA-Protein with one or more restrictionenzymes so as to generate a plurality of DNA-protein complexescomprising sticky ends; filling in the sticky ends with nucleotidescontaining one or more markers, such as biotin, to create blunt endsthat are then ligated together; fragmenting the plurality of DNA-proteincomplexes into fragments; pulling down junction containing fragments byusing the one or more of the markers; and sequencing the junctioncontaining fragments using high throughput sequencing methods togenerate a plurality of read pairs. In a further embodiment, theplurality of read pairs for the methods disclosed herein is generatedfrom data produced by probing the physical layout of chromatin.

In a particular embodiment, the disclosure provides that a plurality ofread pairs can be determined by probing the physical layout ofchromosomes or chromatin isolated from cultured cells or primary tissue.In an alternate embodiment, the plurality of read pairs can bedetermined by probing the physical layout of reconstituted chromatinformed by complexing naked DNA obtained from a sample of one or moresubjects with isolated histones.

In another embodiment, the disclosure provides a method to determinehaplotype phasing comprising a step of identifying one or more sites ofheterozygosity in the plurality of read pairs, wherein phasing data forallelic variants can be determined by identifying read pairs thatcomprise a pair of heterozygous sites.

In a certain embodiment, the disclosure provides a method forhigh-throughput bacterial genome assembly, comprising a step ofgenerating a plurality of read pairs by probing the physical layout of aplurality of microbial chromosomes using a modified Hi-C based method,comprising the modified steps of: collecting microbes from anenvironment; adding a fixative agent, such as formaldehyde, so as toform cross-links within each microbial cell, and wherein read pairsmapping to different contigs indicate which contigs are from the samespecies.

INCORPORATION BY REFERENCE

All publications, patents, and patent applications mentioned in thisspecification are herein incorporated by reference to the same extent asif each individual publication, patent, or patent application wasspecifically and individually indicated to be incorporated by reference.All publications, patents, and patent applications mentioned in thisspecification are herein incorporated by reference in its entirety aswell as any references cited therein.

BRIEF DESCRIPTION OF THE DRAWINGS

The novel features of the disclosure are set forth with particularity inthe appended claims. A better understanding of the features andadvantages of the disclosure will be obtained by reference to thefollowing detailed description that sets forth illustrative embodiments,in which the principles of the disclosure are utilized, and theaccompanying drawings of which:

FIG. 1 presents an illustration of genome assembly using high-throughputsequencing reads. The genome to be assembled is shown (top). Typically,genomes have many repeat sequences that are difficult to assemble.Random, high-throughput sequence data from genomes (middle) arecollected and assembled into “contigs” in regions that are unique in thegenome (bottom). Contig assembly generally stops at the many repeatsequences. The final output is a set of thousands of contigs whose orderand orientation relative to one another are not known. In the figure,they are arbitrarily numbered from longest to shortest.

FIG. 2A-D illustrates a Hi-C based protocol of the disclosure: (A)demonstrates where DNA is cross-linked and processed to createdbiotinylated junction fragments for sequencing; and (B-D) providecontact map data on human chr14 for a variety of restriction enzymes. Asshown, most contacts are local along the chromosome.

FIG. 3 provides a tracing of the distribution of intra-chromosomalread-pair distances using a Hi-C based protocol of the disclosure. Eightdatasets are shown. In each dataset, the frequency of read-pairsdecreases exponentially with increasing distance such that read pairsare more likely to be separated by a smaller distance than a longerdistance. As shown, there is a long tail of read-pair distances thatextends over hundreds of kilobases.

FIG. 4A-C provides a method of the disclosure using Hi-C sequence datato assist genome assembly: (A) illustrates where DNA is cross-linked andprocessed using a Hi-C based protocol; (B) demonstrates where read-pairdata is mapped to assembled contigs, generated from random shotgunsequencing and assembly; and (C) illustrates that after filtering andweighting, an adjacency matrix summarizing all inter-contig read pairdata can be constructed. This matrix can be re-ordered to indicate thecorrect assembly path. As shown, most of the read pairs will map withina contig. From which, it is possible to learn the distribution ofcontact distances (e.g., see FIG. 3). Read pairs that map to differentcontigs provide data about which contigs are adjacent in a correctgenome assembly.

DETAILED DESCRIPTION

As used herein and in the appended claims, the singular forms “a,”“and,” and “the” include plural referents unless the context clearlydictates otherwise. Thus, for example, reference to “contig” includes aplurality of such contigs and reference to “probing the physical layoutof chromosomes” includes reference to one or more methods for probingthe physical layout of chromosomes and equivalents thereof known tothose skilled in the art, and so forth.

Also, the use of “and” means “and/or” unless stated otherwise.Similarly, “comprise,” “comprises,” “comprising” “include,” “includes,”and “including” are interchangeable and not intended to be limiting.

It is to be further understood that where descriptions of variousembodiments use the term “comprising,” those skilled in the art wouldunderstand that in some specific instances, an embodiment can bealternatively described using language “consisting essentially of” or“consisting of.”

The term “sequencing read” as used herein, refers to a fragment of DNAin which the sequence has been determined.

The term “contigs” as used herein, refers to contiguous regions of DNAsequence. “Contigs” can be determined by any number methods known in theart, such as, by comparing sequencing reads for overlapping sequences,and/or by comparing sequencing reads against a databases of knownsequences in order to identify which sequencing reads have a highprobability of being contiguous.

The term “subject” as used herein can refer to any eukaryotic orprokaryotic organism.

The term “naked DNA” as used herein refers to DNA that is substantiallyfree of complexed proteins.

The term “reconstituted chromatin” as used herein refers to formingchromatin by complexing isolated nuclear proteins to naked DNA.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood to one of ordinary skill inthe art to which this disclosure belongs. Although any methods andreagents similar or equivalent to those described herein can be used inthe practice of the disclosed methods and compositions, the exemplarymethods and materials are now described.

Basic evolutionary and biomedical research is being driven bytechnological advances in high-throughput sequencing. Whereas wholegenome sequencing and assembly used to be the provenance of large genomesequencing centers, commercially available sequencers are nowinexpensive enough that most research universities have one or severalof these machines. It is now relatively inexpensive to generate massivequantities of DNA sequence data. However it remains difficult in theoryand in practice to produce high-quality, highly contiguous genomesequences with current technology. Furthermore, because most organismsthat one would care to analyze, including humans, are diploid, eachindividual has two copies of the genome. At sites of heterozygosity(where the allele given by the mother differs from the allele given bythe father), it is difficult to know which sets of alleles came fromwhich parent (known as haplotype phasing). This information can be usedfor many kinds of evolutionary and biomedical studies such as diseaseand trait association studies.

The disclosure provides methods for genome assembly that combinetechnologies for DNA preparation with paired-end sequencing forhigh-throughput discovery of short, intermediate and long termconnections within a given genome. The disclosure further providesmethods using these connections to assist in genome assembly, forhaplotype phasing, and/or for metagenomic studies. While the methodspresented herein can be used to determine the assembly of a subject'sgenome, it should also be understood that the methods presented hereincan also be used to determine the assembly of portions of the subject'sgenome such as chromosomes, or the assembly of the subject's chromatinof varying lengths.

In a particular embodiment, the disclosure provides for one or moremethods disclosed herein that comprise the step of generating aplurality of contigs from sequencing fragments of target DNA obtainedfrom a subject. Long stretches of target DNA can be fragmented bycutting the DNA with one or more restriction enzymes, shearing the DNA,or a combination thereof. The resulting fragments can be sequenced usinghigh throughput sequencing methods to obtain a plurality of sequencingreads. Examples of high throughput sequencing methods which can be usedwith the methods of the disclosure include, but are not limited to, 454pyrosequencing methods developed Roche Diagnostics, “clusters”sequencing methods developed by Illumina, SOLiD and Ion semiconductorsequencing methods developed by Life Technologies, and DNA nanoballsequencing methods developed by Complete Genomics. Overlapping ends ofdifferent sequencing reads can then be assembled to form a contig.Alternatively, fragmented target DNA can be cloned into vectors. Cellsor organisms are then transfected with the DNA vectors to form alibrary. After replicating the transfected cells or organisms, thevectors are isolated and sequenced to generate a plurality of sequencingreads. The overlapping ends of different sequencing reads can then beassembled to form a contig.

As shown in FIG. 1, genome assembly, especially with high-throughputsequencing technology can be problematic. Often, the assembly consistsof thousands or tens of thousands of short contigs. The order andorientation of these contigs is generally unknown, limiting theusefulness of the genome assembly. Technologies exist to order andorient these scaffolds, but they are generally expensive, laborintensive, and often fail in discovering very long range interactions.

As will be appreciated by those in the art, samples comprising targetDNA used to generate contigs can be obtained from a subject by anynumber of means, including by taking bodily fluids (e.g., blood, urine,serum, lymph, saliva, anal and vaginal secretions, perspiration andsemen), taking tissue, or by collecting cells/organisms. The sampleobtained may be comprised of a single type of cell/organism, or may becomprised multiple types of cells/organisms. The DNA can be extractedand prepared from the subject's sample using known techniques. Forexample, the sample may be treated to lyse a cell comprising thepolynucleotide, using known lysis buffers, sonication techniques,electroporation, and the like. The target DNA may be further purified toremove contaminants, such as proteins, by using alcohol extractions,cesium gradients, and/or column chromatography.

In a particular embodiment, the disclosure provides for one or moremethods disclosed herein that comprise the step of probing the physicallayout of chromosomes within living cells. Examples of techniques toprobe the physical layout of chromosomes through sequencing include the“C” family of techniques, such as chromosome conformation capture(“3C”), circularized chromosome conformation capture (“4C”), carbon-copychromosome capture (“5C”), and Hi-C based methods; and ChIP basedmethods, such as ChIP-loop, ChIP-PET. In a certain embodiment, one ormore methods disclosed herein utilize Hi-C based techniques to probe thephysical layout of chromosomes, chromatin, or reconstituted chromatin.

A Hi-C based technique is summarized in FIG. 2. In brief, cross-linksare created between genome regions that are in close physical proximity.Crosslinking of proteins (such as histones) to the DNA within chromatincan be accomplished according to various methods. One approach is toexpose the chromatin to ultraviolet irradiation. Other approachesutilize chemical crosslinking agents. Suitable chemical crosslinkingagents include, but are not limited to, formaldehyde and psoralen. TheDNA may be immunoprecipitated prior to or after crosslinking. Suchmethods generally involve fragmenting chromatin and then contacting thefragments with an antibody that specifically recognizes and binds toacetylated histones, particularly H3. Examples of such antibodiesinclude, but are not limited to, Anti Acetylated Histone H3, availablefrom Upstate Biotechnology, Lake Placid, N.Y. The polynucleotides fromthe immunoprecipitate can subsequently be collected from theimmunoprecipitate. Prior to fragmenting the chromatin, one canoptionally crosslink the acetylated histones to adjacent DNA. Themixture is then treated to fractionate polynucleotides in the mixture.Fractionation techniques are known in the art and include, for example,shearing techniques to generate smaller genomic fragments. Fragmentationcan be accomplished using established methods for fragmenting chromatin,including, for example, sonication, shearing and/or the use ofrestriction enzymes. The resulting fragments can vary in size. In oneembodiment, using sonication techniques, fragments of approximately200-400 nucleotides can be obtained. Then, a series of steps isperformed that creates a single, short stretch of DNA that is a ligationproduct between the two regions that were originally in close physicalproximity. These ligation products are then subjected to paired-endsequencing (the beginning and end of each fragment is sequenced) usinghigh-throughput sequencing. Each read pair represents a single pair ofgenomic regions that were in close physical proximity.

One feature of the data generated by Hi-C is that most reads pairs, whenmapped back to the genome, are found to be in close linear proximity.That is, most read pairs are found to be close to one another in thegenome. In detecting long-range intra-chromosomal and especiallyinter-chromosomal contacts, this “background” of short and intermediaterange intra-chromosomal contacts are background noise to be factored outusing Hi-C analysis.

Examination of the physical distance between intra-chromosomal readpairs indicates several useful features of the data with respect togenome assembly. First, shorter range interactions are more common thanlonger-range interactions (e.g., see FIG. 3). That is, each read of aread-pair is more likely to be mated with a region close by in theactual genome than it is to be with a region that is far away. Second,there is a long tail of intermediate and long-range interactions. Thatis, read-pairs carry information about intra-chromosomal arrangement atmegabase (Mb) distances. These features of the data simply indicate thatregions of the genome that are nearby on the same chromosome are morelikely to be in close physical proximity—an expected result because theyare chemically linked to one another through the DNA backbone.

Universally, procedures for probing the physical layout of chromosomes,such as Hi-C based techniques, utilize chromatin that is formed within acell/organism, such as chromatin isolated from cultured cells or primarytissue. The disclosure provides not only for the use of such techniqueswith chromatin isolated from a cell/organism but also with reconstitutedchromatin. Reconstituted chromatin has many benefits over chromatinformed within a cell/organism. First, for many samples, the collectionof naked DNA samples can be achieved by using a variety of noninvasiveto invasive methods, such as by collecting bodily fluids, swabbingbuccal or rectal areas, taking epithelial samples, etc. Moreover, it maybe impractical or impossible to successfully culture certain types ofcells long-term. Second, reconstituted chromatin will not have theinter-chromosomal and other long-range interactions that generateartifacts for genome assembly and haplotype phasing. Third, by varyingthe ratio of DNA to histones, it is possible to reduce the nucleosomedensity. In this way, crosslinks will naturally favor longer-rangeinteractions. As shorter range contacts are disfavored and longer rangecontacts favored, the usefulness for contig ordering will be increased.

In a particular embodiment, the disclosure provides for one or moremethods disclosed herein that comprise the step of mapping the pluralityof read pairs to the plurality of contigs. Most of the read pairs willmap within in a contig, and from which the distribution of distancesbetween read pairs can be learned, and from which an adjacency matrix ofcontigs can be constructed using read pairs that map to differentcontigs.

In a certain embodiment, the disclosure provides for one or more methodsdisclosed herein that comprise the step of constructing an adjacencymatrix of contigs using the read-mapping data from the read-pair data.In another embodiment, the adjacency matrix uses a weighting scheme forread pairs that incorporate the tendency for short-range interactionsover long-range interactions (e.g., see FIG. 4). In a furtherembodiment, the adjacency matrix can further be re-scaled to down-weightthe high number of contacts on some contigs that represent promiscuousregions of the genome. In yet a further embodiment, this scaling can bedirected by searching for one or more conserved binding sites for one ormore agents that regulate the scaffolding interactions of chromatin,such as transcriptional repressor CTCF.

In particular embodiment, the disclosure provides for one or moremethods disclosed herein that comprise a step of analyzing the adjacencymatrix to determine a path through the contigs that represent theirorder and/or orientation to the genome. In another embodiment, the paththrough the contigs is chosen so that each contig is visited exactlyonce. In a further embodiment, the path through the contigs is chosen sothat edge-weighting of adjacency matrix is maximized. In yet a furtherembodiment, the path through the contigs is chosen so that each contigis visited exactly once and that edge-weighting of adjacency matrix ismaximized.

In diploid genomes, it often important to know which allelic variantsare linked on the same chromosome. This is known as the haplotypephasing. Short reads from high-throughput sequence data rarely allow oneto directly observe which allelic variants are linked. Computationalinference of haplotype phasing is unreliable at long distances. Thedisclosure provides one or methods that allow for determining whichallelic variants are linked using allelic variants on read pairs.

Humans are heterozygous at an average of 1 site in 1,000. A lane of datausing high throughput sequencing methods can generate about 150,000,000read pairs. Each read pair is 100 base pairs long. From theseparameters, it is estimated that one-tenth of all reads will cover aheterozygous site. Thus, on average one-hundredth of all read pairs willcover a pair of heterozygous sites. These 1,500,000 read pairs(one-hundredth of 150,000,000) provide phasing data. Because there areapproximately 3 billion bases in the human genome and one inone-thousand is heterozygous, there are approximately 3 millionheterozygous sites in a human genome. Each read-pair reveals phase datathat covers a pair of heterozygous sites. As there are 1,500,000 suchread pairs, the average coverage of each heterozygous site to be phasedusing high throughput sequence method accounts for one lane of data (1×)using typical high throughput sequencing machines. A genome cantherefore be reliably and completely phased with one lane of Hi-Csequence data using the methods disclosed herein.

One current avenue of research, meta-genomics, investigates the DNAsequence of all organisms that inhabit a given ecological environment.Examples include random sequencing of all gut microbes, the microbesfound on certain areas of skin, and the microbes that live in toxicwaste sites. These studies have revealed a lot about the composition ofthe microbe population in these environments and embodiments ofinterrelated biochemistries encoded by their respective genomes.However, metagenomic studies are all hampered by the complexity of thebiological environments. Generally, there are too many species with toomuch genome variability to attempt to assemble genomes from the randomdata recovered. The disclosure provides one or more methods that allowfor the assembly of genomes for metagenomic projects.

The following examples are intended to illustrate but not limit thedisclosure. While they are typical of those that might be used, otherprocedures known to those skilled in the art may alternatively be used.

EXAMPLES

Methods to Generate Chromatin In Vitro:

Two approaches to reconstitute chromatin include (1) to useATP-independent random deposition of histones onto DNA, while the other(2) uses ATP-dependent assembly of periodic nucleosomes. The disclosureallows the use of either approach with one or more methods disclosedherein. Examples of both approaches to generate chromatin can be foundin Lusser et al. (“Strategies for the reconstitution of chromatin,”Nature Methods (2004), 1(1):19-26), which is incorporated herein byreference in its entirety, including the references cited therein.

Genome Assembly Using HI-C Based Techniques:

A genome from a human subject was fragmented into pseudo-contigs havinga size of 500 kb. Using a Hi-C based method, a plurality of read pairswere generated by probing the physical layout of chromosomes withinliving cells. Any number of Hi-C based methods can be used to generateread pairs, including the method presented in Lieberman-Aiden et al.(“Comprehensive mapping of long range interactions reveals foldingprinciples of the human genome,” Science (2009), 326(5950):289-293),which is incorporated herein in-full, including the references citedtherein. Read pairs were mapped to all pseudo-contigs and those pairsthat mapped to two separate pseudo-contigs, were used to construct anadjacency matrix based upon the mapping data. Each read pair wasweighted by taking a function of each read's distance to the edge of thepseudo-contig so as to mathematically incorporate the empirically knownhigher probability of shorter contacts than longer contacts. Then, foreach pseudo-contig, the adjacency matrix was analyzed to determine apath through the pseudo-contigs by finding the single best neighborpseudo-contig, which was determined by having the highestsum-of-weights. By performing these methods, it was found that >97% ofall pseudo-contigs identified their correct neighbor. Additionalexperiments can be performed to test the impact of shorter contigs andalternate weighting and path-finding schemes.

Methods for Haplotype Phasing:

Because the read pairs generated by the methods disclosed herein aregenerally derived from intra-chromosomal contacts, any read pairs thatcontain sites of heterozygosity will also carry information about theirphasing. Using this information, reliable phasing over short,intermediate and even long (megabase) distances can be performed rapidlyand accurately. Experiments designed to phase data from one of the 1000genomes trios (a set of mother/father/offspring genomes) have reliablyinferred phasing.

Methods for Meta-Genomic Assembly:

Microbes are collected from an environment and fixed with a fixativeagent, such as formaldehyde, in order to form cross-links within eachmicrobial cell. A plurality of contigs from each microbe is generated byusing high-throughput sequencing. A plurality of read pairs aregenerated by using Hi-C based techniques. Read pairs that map todifferent contigs indicate which contigs are from the same species.

While preferred embodiments of the disclosure have been shown anddescribed herein, it will be obvious to those skilled in the art thatsuch embodiments are provided by way of example only. Numerousvariations, changes, and substitutions will now occur to those skilledin the art without departing from the disclosure. It should beunderstood that various alternatives to the embodiments of thedisclosure described herein may be employed in practicing thedisclosure. It is intended that the following claims define the scope ofthe disclosure and that methods and structures within the scope of theseclaims and their equivalents be covered thereby.

What is claimed is:
 1. A method of genome assembly, comprising:contacting a sample to a stabilizing agent, said sample comprising anucleic acid molecule complexed to at least one nucleic acid bindingprotein; cleaving the nucleic acid into a plurality of segmentscomprising at least a first segment and a second segment; attaching thefirst segment and the second segment at a junction; obtaining at leastsome sequence on each side of the junction to generate a first readpair; mapping the first read pair to a set of contigs; and determining apath through the set of contigs that represents an order and/ororientation to a genome.
 2. The method of claim 1, comprising: excludingthe first read pair from contig assembly analysis because said at leastsome sequence on each side of the junction maps to a common contig; anddetermining a path through the contigs that represents an order and/ororientation to the genome using a second read pair.
 3. The method ofclaim 1, comprising: contacting the sample to an antibody prior tocontacting the sample to the stabilizing agent.
 4. The method of claim1, comprising: contacting the sample to an antibody subsequent tocontacting the sample to the stabilizing agent.
 5. The method of claim1, wherein cleaving the nucleic acid into at least a first segment and asecond segment comprises cutting the nucleic acid using at least onerestriction enzyme.
 6. The method of claim 1, wherein cleaving thenucleic acid into at least a first segment and a second segmentcomprises shearing the nucleic acid.
 7. The method of claim 1, whereincleaving the nucleic acid into at least a first segment and a secondsegment comprises sonicating the nucleic acid.
 8. The method of claim 1,wherein contacting a sample to a stabilizing agent comprisesadministering ultraviolet light.
 9. The method of claim 1, whereincontacting a sample to a stabilizing agent comprises contacting thesample to a chemical fixative.
 10. The method of claim 9, wherein thechemical fixative comprises formaldehyde.
 11. The method of claim 9,wherein the chemical fixative comprises psoralen.
 12. The method ofclaim 1, wherein the at least one nucleic acid binding protein comprisesa native chromatin constituent.
 13. The method of claim 1, wherein theat least one nucleic acid binding protein comprises an exogenouslysupplied histone.
 14. The method of claim 1, wherein attaching comprisesfilling in sticky ends using at least some biotin tagged nucleotides andligating the blunt ends.
 15. The method of claim 1, wherein the paththrough the set of contigs that represents an order and/or orientationto the genome is determined so that each contig is visited exactly once.16. The method of claim 1, wherein determining a path through the set ofcontigs that represents an order and/or orientation to the genomecomprises down-weighing contigs that represent promiscuous regions ofthe genome.
 17. The method of claim 1, wherein the set of contigs isgenerated by a shotgun sequencing method.
 18. The method of claim 1,wherein determining a path through the set of contigs that represents anorder and/or orientation to the genome comprises haplotype phasing theset of contigs.
 19. The method of claim 18, wherein haplotype phasingthe set of contigs comprise identifying one or more sites ofheterozygosity in a plurality of read pair sequences, wherein phasingdata for allelic variants is determined by identifying read pairs thatcomprise a pair of heterozygous sites.
 20. The method of claim 1,comprising excluding from analysis read pair sequence that maps to acommon contig, so as to determine a path through the set of contigs thatrepresents an order and/or orientation to the genome using read pairsthat map to different contigs.